/usr/include/OpenMS/ANALYSIS/DECHARGING/ILPDCWrapper.h is in libopenms-dev 1.11.1-5.
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// OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2013.
//
// This software is released under a three-clause BSD license:
// * Redistributions of source code must retain the above copyright
// notice, this list of conditions and the following disclaimer.
// * Redistributions in binary form must reproduce the above copyright
// notice, this list of conditions and the following disclaimer in the
// documentation and/or other materials provided with the distribution.
// * Neither the name of any author or any participating institution
// may be used to endorse or promote products derived from this software
// without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
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// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $Maintainer: Chris Bielow $
// $Authors: Chris Bielow $
// --------------------------------------------------------------------------
#ifndef OPENMS_ANALYSIS_DECHARGING_ILPDCWRAPPER_H
#define OPENMS_ANALYSIS_DECHARGING_ILPDCWRAPPER_H
#include <vector>
#include <OpenMS/DATASTRUCTURES/ChargePair.h>
namespace OpenMS
{
class MassExplainer;
class OPENMS_DLLAPI ILPDCWrapper
{
public:
typedef std::vector<ChargePair> PairsType;
typedef PairsType::size_type PairsIndex;
///Constructor
ILPDCWrapper();
///Destructor
virtual ~ILPDCWrapper();
/// Compute optimal solution and return value of objective function
/// If the input feature map is empty, a warning is issued and -1 is returned.
/// @return value of objective function
/// and @p pairs will have all realized edges set to "active"
DoubleReal compute(const FeatureMap<> fm, PairsType & pairs, Size verbose_level) const;
private:
/// slicing the problem into subproblems
DoubleReal computeSlice_(const FeatureMap<> fm,
PairsType & pairs,
const PairsIndex margin_left,
const PairsIndex margin_right,
const Size verbose_level) const;
/// slicing the problem into subproblems
DoubleReal computeSliceOld_(const FeatureMap<> fm,
PairsType & pairs,
const PairsIndex margin_left,
const PairsIndex margin_right,
const Size verbose_level) const;
/// calculate a score for the i_th edge
DoubleReal getLogScore_(const PairsType::value_type & pair, const FeatureMap<> & fm) const;
typedef Map<String, std::set<Size> > FeatureType_;
// add another charge annotation variant for a feature
void updateFeatureVariant_(FeatureType_ & f_set, const String & rota_l, const Size & v) const;
}; // !class
} // !namespace
#endif // OPENMS_ANALYSIS_DECHARGING_ILPDCWRAPPER_H
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